Analyze and visualize VDJ data with Seurat

Author: Biqing Li

May 6, 2020

Outline

Quality control

Highly variable genes

PCA

UMAP

0 1 2 3 4 5 6 7 8 9
cell.freq 0.24 0.24 0.17 0.11 0.1 0.07 0.03 0.01 0.01 0.01
cell.num 641.00 636.00 451.00 280.00 257.0 176.00 78.00 38.00 38.00 22.00

TSNE

Markers for each cluster

cluster0 cluster1 cluster2 cluster3 cluster4 cluster5 cluster6 cluster7 cluster8 cluster9
IL7R GNLY S100A9 CD8B IGKC CXCR3 C1QA CCR7 MCM2 FCER1A
PIK3IP1 KLRF1 S100A12 CD8A IGHM-membrane GZMK IL3RA IL7R TYMS CLEC10A
LEF1 GZMB CD14 KLRK1 CD79A IL32 PTGDR2 PIK3IP1 TRAT1 FLT3
TCF7 PRF1 IER3 CCL5 IGHD-membrane IL7R TNFRSF8 LTB PIK3IP1 CD1C
CCR7 IL2RB FCN1 TARP-refseq IGHM-secreted CD3E CXCL16 LEF1 TCF7 IL18
CD6 NKG7 CXCL8 GZMK MS4A1 CD2.1 FCGR3A CD6 LEF1 HLA-DRA
CD5 TBX21 CLEC4E IL32 CD22 CD6 LYN CD3D GIMAP2 CD33
CD27 TRDC CD163 GZMH VPREB3 CD3D BCL2A1 GIMAP5 TRIB2 HLA-DQB1
LTB IL18RAP CD36 GZMA IGLC3 LTB PIK3AP1 PASK MYC HLA-DMA
MYC CD160 CCL3 KLRG1 TCL1A CD3G IFITM3 MYC PCNA HLA-DPA1

Violin plot for classical markers

Dotplot plot for classical markers

RidgePlot plot for classical markers

Feature plot for classical markers

Assigning cell type identity to clusters

Heatmap

3D UMAP

3D UMAP gif

All paired B & T cells

B cell & BCR

T_CD4_memory & TCR

T_CD4_naive & TCR

T_CD8_memory & TCR

T_CD8_naive & TCR

T_gamma_delta & TCR

B cell VDJ genotype

Gamma delta T cell VDJ genotype

Thank you!